chr3-193618850-T-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_130837.3(OPA1):c.611-19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 1,593,068 control chromosomes in the GnomAD database, including 149,138 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.43 ( 14298 hom., cov: 32)
Exomes 𝑓: 0.43 ( 134840 hom. )
Consequence
OPA1
NM_130837.3 intron
NM_130837.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.02
Genes affected
OPA1 (HGNC:8140): (OPA1 mitochondrial dynamin like GTPase) The protein encoded by this gene is a nuclear-encoded mitochondrial protein with similarity to dynamin-related GTPases. The encoded protein localizes to the inner mitochondrial membrane and helps regulate mitochondrial stability and energy output. This protein also sequesters cytochrome c. Mutations in this gene have been associated with optic atrophy type 1, which is a dominantly inherited optic neuropathy resulting in progressive loss of visual acuity, leading in many cases to legal blindness. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 3-193618850-T-C is Benign according to our data. Variant chr3-193618850-T-C is described in ClinVar as [Benign]. Clinvar id is 95728.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-193618850-T-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OPA1 | NM_130837.3 | c.611-19T>C | intron_variant | ENST00000361510.8 | NP_570850.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OPA1 | ENST00000361510.8 | c.611-19T>C | intron_variant | 5 | NM_130837.3 | ENSP00000355324.2 |
Frequencies
GnomAD3 genomes AF: 0.430 AC: 65259AN: 151804Hom.: 14285 Cov.: 32
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GnomAD3 exomes AF: 0.425 AC: 106737AN: 251250Hom.: 23228 AF XY: 0.421 AC XY: 57202AN XY: 135794
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GnomAD4 exome AF: 0.429 AC: 618431AN: 1441146Hom.: 134840 Cov.: 28 AF XY: 0.427 AC XY: 306556AN XY: 718102
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GnomAD4 genome AF: 0.430 AC: 65315AN: 151922Hom.: 14298 Cov.: 32 AF XY: 0.432 AC XY: 32057AN XY: 74258
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 01, 2011 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 23, 2015 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at